Optimising the Definition of Expressed Regions


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Documentation for package ‘ODER’ version 1.6.0

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add_expressed_genes Adding the nearest expressed genes
annotatERs Connects ERs to genes using junction data, then classifies ERs into "exonic", "intronic", "intergenic", or a combination of these categories
file_cache Cache a file if it is not found locally
get_chr_info Get information from UCSC about the chromosomes passed in
get_count_matrix Generate the count matrix
get_coverage Obtain the mean coverage across multiple BigWig files
get_ers Define sets of ERs
get_ers_delta Obtain set of non-overlapping exons
get_exons Obtain set of non-overlapping exons
get_opt_ers Obtain set of non-overlapping exons
get_strand_ers Define sets of ERs
gtex_SRP012682_SRX222703_lung_auc_1 An example AUC value
gtex_SRP012682_SRX222703_lung_coverage_1 An example object containing coverage
gtex_SRP012682_SRX222703_lung_erdelta_1 An example set of ER deltas
gtex_SRP012682_SRX222703_lung_ers_1 An example set of Expressed Regions
lung_junc_21_22 Junction data of chromosomes 21 and 22 from a lung tissue sample
ODER ODER: Optimising the Definition of Expressed Regions
plot_ers Plot Expressed regions
pseudogene Different transcript biotypes that count as pseudogene
refine_ERs Refines the ERs start and end points
tissue_options The different tissues that can be filtered on for gene expression